AUTHOR=Odonkor Sandra , Choi Soyeon , Chakraborty Debkanta , Martinez-Bello Liliam , Wang Xuewen , Bahri Bochra A. , Tenaillon Maud I. , Panaud Olivier , Devos Katrien M. 

TITLE=QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica

JOURNAL=Frontiers in Plant Science

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2018.00918

DOI=10.3389/fpls.2018.00918

ISSN=1664-462X

ABSTRACT=<p><italic>Setaria</italic> (L.) P. Beauv is a genus of grasses that belongs to the <italic>Poaceae</italic> (grass) family, subfamily Panicoideae. Two members of the <italic>Setaria</italic> genus, <italic>Setaria italica</italic> (foxtail millet) and <italic>S. viridis</italic> (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for <italic>S. italica</italic> and its wild progenitor, <italic>S. viridis</italic>, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F<sub>2:3</sub> and recombinant inbred line (RIL) populations generated from a cross between <italic>S. italica</italic> accession B100 and <italic>S. viridis</italic> accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild <italic>S. viridis</italic>. Comparative analyses pinpointed <italic>Sh1</italic> and <italic>qSH1</italic>, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on <italic>Setaria</italic> chromosomes IX and V, respectively. The <italic>Sh1</italic> allele in <italic>S. italica</italic> was shown to carry a <italic>PIF/Harbinger</italic> MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in <italic>S. italica</italic> accessions around the world and absent from the <italic>S. viridis</italic> germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The <italic>qSH1</italic> gene carried two MITEs in the 5′UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in <italic>qSH1</italic> played a role in reducing shattering in <italic>S. italica</italic> accessions, selection for the variants likely occurred after the domestication of foxtail millet.</p>